Showing papers by "Dublin City University published in 2013"

Cloud Migration Research: A Systematic Review

Abstract: Background--By leveraging cloud services, organizations can deploy their software systems over a pool of resources. However, organizations heavily depend on their business-critical systems, which have been developed over long periods. These legacy applications are usually deployed on-premise. In recent years, research in cloud migration has been carried out. However, there is no secondary study to consolidate this research. Objective--This paper aims to identify, taxonomically classify, and systematically compare existing research on cloud migration. Method--We conducted a systematic literature review (SLR) of 23 selected studies, published from 2010 to 2013. We classified and compared the selected studies based on a characterization framework that we also introduce in this paper. Results--The research synthesis results in a knowledge base of current solutions for legacy-to-cloud migration. This review also identifies research gaps and directions for future research. Conclusion--This review reveals that cloud migration research is still in early stages of maturity, but is advancing. It identifies the needs for a migration framework to help improving the maturity level and consequently trust into cloud migration. This review shows a lack of tool support to automate migration tasks. This study also identifies needs for architectural adaptation and self-adaptive cloud-enabled systems.

Correlating transcriptional networks to breast cancer survival: a large-scale coexpression analysis

Abstract: Weighted gene coexpression network analysis (WGCNA) is a powerful 'guilt-by-association'-based method to extract coexpressed groups of genes from large heterogeneous messenger RNA expression data sets. We have utilized WGCNA to identify 11 coregulated gene clusters across 2342 breast cancer samples from 13 microarray-based gene expression studies. A number of these transcriptional modules were found to be correlated to clinicopathological variables (e.g. tumor grade), survival endpoints for breast cancer as a whole (disease-free survival, distant disease-free survival and overall survival) and also its molecular subtypes (luminal A, luminal B, HER2+ and basal-like). Examples of findings arising from this work include the identification of a cluster of proliferation-related genes that when upregulated correlated to increased tumor grade and were associated with poor survival in general. The prognostic potential of novel genes, for example, ubiquitin-conjugating enzyme E2S (UBE2S) within this group was confirmed in an independent data set. In addition, gene clusters were also associated with survival for breast cancer molecular subtypes including a cluster of genes that was found to correlate with prognosis exclusively for basal-like breast cancer. The upregulation of several single genes within this coexpression cluster, for example, the potassium channel, subfamily K, member 5 (KCNK5) was associated with poor outcome for the basal-like molecular subtype. We have developed an online database to allow user-friendly access to the coexpression patterns and the survival analysis outputs uncovered in this study (available at http://glados.ucd.ie/Coexpression/).

Adsorption and desorption of methylene blue on porous carbon monoliths and nanocrystalline cellulose.

Abstract: The dynamic batch adsorption of methylene blue (MB), a widely used and toxic dye, onto nanocrystalline cellulose (NCC) and crushed powder of carbon monolith (CM) was investigated using the pseudo-first- and -second-order kinetics. CM outperformed NCC with a maximum capacity of 127 mg/g compared to 101 mg/g for NCC. The Langmuir isotherm model was applicable for describing the binding data for MB on CM and NCC, indicating the homogeneous surface of these two materials. The Gibbs free energy of −15.22 kJ/mol estimated for CM unravelled the spontaneous nature of this adsorbent for MB, appreciably faster than the use of NCC (−4.47 kJ/mol). Both pH and temperature exhibited only a modest effect on the adsorption of MB onto CM. The desorption of MB from CM using acetonitrile was very effective with more than 94 % of MB desorbed from CM within 10 min to allow the reusability of this porous carbon material. In contrast, acetonitrile was less effective than ethanol in desorbing MB from NCC. The two solvents were i...

Stimuli responsive synthetic polypeptides derived from N-carboxyanhydride (NCA) polymerisation

Abstract: The progress in NCA polymerisation combined with advanced orthogonal functionalization techniques as well as the integration with other controlled polymerisation techniques significantly widened the scope of polypeptide building blocks in a variety of material designs. Well-defined synthetic stimuli-responsive polypeptides (“smart” polypeptides) with incorporated different functionalities have been extensively explored over the past decades. Their significant potential lies in the fact that they combine natural and synthetic elements both contributing to their properties. These novel materials have potential applications in biomedicine and biotechnology including tissue engineering, drug delivery and biodiagnostics. Responsive polypeptides are capable of undergoing conformational changes and phase transition accompanied by variations in the chemical and physical changes of the polypeptides in response to an external stimulus such as biologically relevant species (i.e. biomolecules), the environment (i.e. temperature, pH), irradiation with light or exposure to a magnetic field. In this review, the recent developments including synthetic strategies and applications of synthetic stimuli-responsive homo- and block polypeptides are reviewed.

Overview of the ShARe/CLEF eHealth Evaluation Lab 2013

Abstract: Discharge summaries and other free-text reports in healthcare transfer information between working shifts and geographic locations. Patients are likely to have difficulties in understanding their content, because of their medical jargon, non-standard abbreviations, and ward-specific idioms. This paper reports on an evaluation lab with an aim to support the continuum of care by developing methods and resources that make clinical reports in English easier to understand for patients, and which helps them in finding information related to their condition. This ShARe/CLEFeHealth2013 lab offered student mentoring and shared tasks: identification and normalisation of disorders 1a and 1b and normalisation of abbreviations and acronyms 2 in clinical reports with respect to terminology standards in healthcare as well as information retrieval 3 to address questions patients may have when reading clinical reports. The focus on patients' information needs as opposed to the specialised information needs of physicians and other healthcare workers was the main feature of the lab distinguishing it from previous shared tasks. De-identified clinical reports for the three tasks were from US intensive care and originated from the MIMIC II database. Other text documents for Task 3 were from the Internet and originated from the Khresmoi project. Task 1 annotations originated from the ShARe annotations. For Tasks 2 and 3, new annotations, queries, and relevance assessments were created. 64, 56, and 55 people registered their interest in Tasks 1, 2, and 3, respectively. 34 unique teams 3 members per team on average participated with 22, 17, 5, and 9 teams in Tasks 1a, 1b, 2 and 3, respectively. The teams were from Australia, China, France, India, Ireland, Republic of Korea, Spain, UK, and USA. Some teams developed and used additional annotations, but this strategy contributed to the system performance only in Task 2. The best systems had the F1 score of 0.75 in Task 1a; Accuracies of 0.59 and 0.72 in Tasks 1b and 2; and Precision at 10 of 0.52 in Task 3. The results demonstrate the substantial community interest and capabilities of these systems in making clinical reports easier to understand for patients. The organisers have made data and tools available for future research and development.

Magnetic core-shell nanoparticles for drug delivery by nebulization

Abstract: Aerosolized therapeutics hold great potential for effective treatment of various diseases including lung cancer. In this context, there is an urgent need to develop novel nanocarriers suitable for drug delivery by nebulization. To address this need, we synthesized and characterized a biocompatible drug delivery vehicle following surface coating of Fe3O4 magnetic nanoparticles (MNPs) with a polymer poly(lactic-co-glycolic acid) (PLGA). The polymeric shell of these engineered nanoparticles was loaded with a potential anti-cancer drug quercetin and their suitability for targeting lung cancer cells via nebulization was evaluated. Average particle size of the developed MNPs and PLGA-MNPs as measured by electron microscopy was 9.6 and 53.2 nm, whereas their hydrodynamic swelling as determined using dynamic light scattering was 54.3 nm and 293.4 nm respectively. Utilizing a series of standardized biological tests incorporating a cell-based automated image acquisition and analysis procedure in combination with real-time impedance sensing, we confirmed that the developed MNP-based nanocarrier system was biocompatible, as no cytotoxicity was observed when up to 100 μg/ml PLGA-MNP was applied to the cultured human lung epithelial cells. Moreover, the PLGA-MNP preparation was well-tolerated in vivo in mice when applied intranasally as measured by glutathione and IL-6 secretion assays after 1, 4, or 7 days post-treatment. To imitate aerosol formation for drug delivery to the lungs, we applied quercitin loaded PLGA-MNPs to the human lung carcinoma cell line A549 following a single round of nebulization. The drug-loaded PLGA-MNPs significantly reduced the number of viable A549 cells, which was comparable when applied either by nebulization or by direct pipetting. We have developed a magnetic core-shell nanoparticle-based nanocarrier system and evaluated the feasibility of its drug delivery capability via aerosol administration. This study has implications for targeted delivery of therapeutics and poorly soluble medicinal compounds via inhalation route.

Simulation benchmarks for low-pressure plasmas: Capacitive discharges

Abstract: Benchmarking is generally accepted as an important element in demonstrating the correctness of computer simulations. In the modern sense, a benchmark is a computer simulation result that has evidence of correctness, is accompanied by estimates of relevant errors, and which can thus be used as a basis for judging the accuracy and efficiency of other codes. In this paper, we present four benchmark cases related to capacitively coupled discharges. These benchmarks prescribe all relevant physical and numerical parameters. We have simulated the benchmark conditions using five independently developed particle-in-cell codes. We show that the results of these simulations are statistically indistinguishable, within bounds of uncertainty that we define. We, therefore, claim that the results of these simulations represent strong benchmarks, which can be used as a basis for evaluating the accuracy of other codes. These other codes could include other approaches than particle-in-cell simulations, where benchmarking could examine not just implementation accuracy and efficiency, but also the fidelity of different physical models, such as moment or hybrid models. We discuss an example of this kind in the Appendix. Of course, the methodology that we have developed can also be readily extended to a suite of benchmarks with coverage of a wider range of physical and chemical phenomena.

Overview of the ShARe/CLEF eHealth Evaluation Lab 2013

Abstract: Discharge summaries and other free-text reports in healthcare transfer information between working shifts and geographic locations. Patients are likely to have difficulties in understanding their content, because of their medical jargon, non-standard abbreviations,and ward-specific idioms. This paper reports on an evaluation lab with an aim to support the continuum of care by developing methods and resources that make clinical reports in English easier to understand for patients, and which helps them in finding information related to their condition.

Aberrant PSA glycosylation—a sweet predictor of prostate cancer

Abstract: Prostate cancer--the most commonly diagnosed cancer in men worldwide--can have a substantial effect on quality of life, regardless of the route the cancer takes. The serum PSA assay is the current gold standard option for diagnosing prostate cancer. However, a growing body of evidence suggests that PSA screening for prostate cancer results in extensive overdiagnosis and overtreatment. It is increasingly evident that the potential harm from overdiagnosis (in terms of unnecessary biopsies) must be weighed against the benefit derived from the early detection and treatment of potentially fatal prostate cancers. Rapid screening methods have been used to analyse glycosylation patterns on glycoproteins in large cohorts of patients, enabling the identification of a new generation of disease biomarkers. Changes to the expression status of certain glycan structures are now widely thought to be common features of tumour progression. In light of this development, much research has focused on the potential role of altered PSA glycosylation patterns in discriminating between significant and insignificant prostate cancers, with the aim of developing a more reliable diagnostic tool than the current serum PSA test.

Genome-wide association study identifies multiple risk loci for chronic lymphocytic leukemia

Abstract: Genome-wide association studies (GWAS) have previously identified 13 loci associated with risk of chronic lymphocytic leukemia or small lymphocytic lymphoma (CLL). To identify additional CLL susceptibility loci, we conducted the largest meta-analysis for CLL thus far, including four GWAS with a total of 3,100 individuals with CLL (cases) and 7,667 controls. In the meta-analysis, we identified ten independent associated SNPs in nine new loci at 10q23.31 (ACTA2 or FAS (ACTA2/FAS), P=1.22×10(-14)), 18q21.33 (BCL2, P=7.76×10(-11)), 11p15.5 (C11orf21, P=2.15×10(-10)), 4q25 (LEF1, P=4.24×10(-10)), 2q33.1 (CASP10 or CASP8 (CASP10/CASP8), P=2.50×10(-9)), 9p21.3 (CDKN2B-AS1, P=1.27×10(-8)), 18q21.32 (PMAIP1, P=2.51×10(-8)), 15q15.1 (BMF, P=2.71×10(-10)) and 2p22.2 (QPCT, P=1.68×10(-8)), as well as an independent signal at an established locus (2q13, ACOXL, P=2.08×10(-18)). We also found evidence for two additional promising loci below genome-wide significance at 8q22.3 (ODF1, P=5.40×10(-8)) and 5p15.33 (TERT, P=1.92×10(-7)). Although further studies are required, the proximity of several of these loci to genes involved in apoptosis suggests a plausible underlying biological mechanism.

CMT-QA: Quality-Aware Adaptive Concurrent Multipath Data Transfer in Heterogeneous Wireless Networks

Abstract: Mobile devices equipped with multiple network interfaces can increase their throughput by making use of parallel transmissions over multiple paths and bandwidth aggregation, enabled by the stream control transport protocol (SCTP) However, the different bandwidth and delay of the multiple paths will determine data to be received out of order and in the absence of related mechanisms to correct this, serious application-level performance degradations will occur This paper proposes a novel quality-aware adaptive concurrent multipath transfer solution (CMT-QA) that utilizes SCTP for FTP-like data transmission and real-time video delivery in wireless heterogeneous networks CMT-QA monitors and analyses regularly each path's data handling capability and makes data delivery adaptation decisions to select the qualified paths for concurrent data transfer CMT-QA includes a series of mechanisms to distribute data chunks over multiple paths intelligently and control the data traffic rate of each path independently CMT-QA's goal is to mitigate the out-of-order data reception by reducing the reordering delay and unnecessary fast retransmissions CMT-QA can effectively differentiate between different types of packet loss to avoid unreasonable congestion window adjustments for retransmissions Simulations show how CMT-QA outperforms existing solutions in terms of performance and quality of service

Thrombomodulin and the vascular endothelium: insights into functional, regulatory, and therapeutic aspects

Abstract: Thrombomodulin (TM) is a 557-amino acid protein with a broad cell and tissue distribution consistent with its wide-ranging physiological roles. When expressed on the lumenal surface of vascular end...

QoE-Driven User-Centric VoD Services in Urban Multihomed P2P-Based Vehicular Networks

Abstract: Recently, many cities around the world have witnessed large-scale deployment of terrestrial broadcasting mobile television (TV) to vehicles. This service is similar to the cable or satellite TV already in the home, and user-centric interactive mobile Video-on-Demand (VoD) over urban vehicular networks is in fact expected. However, providing this new service with focus on user Quality of Experience (QoE) constitutes a significant challenge. This paper introduces a QoE-driven User-centric solution for VoD services in urban vehicular network environments (QUVoD). QUVoD relies on a multihomed hierarchical peer-to-peer (P2P) and vehicular ad-hoc network (VANET) architecture. Vehicles construct a low-layer VANET via Wireless Access in the Vehicular Environment interfaces; they also form an upper layer P2P Chord overlay on top of a cellular network via Fourth-Generation (4G) interfaces. A novel grouping-based storage strategy that uniformly distributes the video segments along the Chord overlay is proposed, reducing segment seeking traffic while also enabling load balancing. A novel segment seeking and multipath delivery scheme that achieves high lookup success rate and very good video data delivery efficiency is also introduced, which achieves high lookup success rate and very good video data delivery efficiency. Furthermore, a new speculation-based prefetching strategy is proposed, which analyses users' interactive viewing behavior and, by estimating video segment playback order, employs prefetching of the expected segments, smoothening the video playback. Simulation results show how QUVoD is a highly efficient user-centric mobile VoD solution in urban vehicular networks in comparison with existing state-of-the-art solutions.

Acquiring and sharing tacit knowledge in software development teams: An empirical study

Abstract: Context Sharing expert knowledge is a key process in developing software products. Since expert knowledge is mostly tacit, the acquisition and sharing of tacit knowledge along with the development of a transactive memory system (TMS) are significant factors in effective software teams. Objective We seek to enhance our understanding human factors in the software development process and provide support for the agile approach, particularly in its advocacy of social interaction, by answering two questions : How do software development teams acquire and share tacit knowledge ? What roles do tacit knowledge and transactive memory play in successful team performance ? Method A theoretical model describing the process for acquiring and sharing tacit knowledge and development of a TMS through social interaction is presented and a second predictive model addresses the two research questions above. The elements of the predictive model and other demographic variables were incorporated into a larger online survey for software development teams, completed by 46 software SMEs, consisting of 181 individual team members. Results Our results show that team tacit knowledge is acquired and shared directly through good quality social interactions and through the development of a TMS with quality of social interaction playing a greater role than transactive memory. Both TMS and team tacit knowledge predict effectiveness but not efficiency in software teams. Conclusion It is concluded that TMS and team tacit knowledge can differentiate between low- and high-performing teams in terms of effectiveness, where more effective teams have a competitive advantage in developing new products and bringing them to market. As face-to-face social interaction is key, collocated, functionally rich, domain expert teams are advocated rather than distributed teams, though arguably the team manager may be in a separate geographic location provided that there is frequent communication and effective use of issue tracking tools as in agile teams.

Promoting Effective Psychological Contracts Through Leadership: The Missing Link Between HR Strategy and Performance

Abstract: This article offers line managers and HR professionals an actionable, research-based framework for developing psychological contracts with employees that suit their organizational and human resource (HR) strategy. Leadership styles supporting the firm's HR strategy are key to making psychological contracts that benefit both the firm and its members. When managers' styles are out of sync with HR strategy, this mismatch can lead to poorer performance through ineffective and unfulfilled psychological contracts with workers.

Seven myths of global talent management

Abstract: The challenges associated with managing talent on a global scale are greater than those faced by organisations operating on a domestic scale. We believe that the former relate to the fact that a number of key myths regarding talent management may undermine talent management's contribution to multinational corporation effectiveness and retard the development of management practice in this regard. Our aim is to unpack some of those myths and offer some suggestions for advancing the practice of talent management on the basis of insights from both practice and academic thinking in this area.

Classification of Sporting Activities Using Smartphone Accelerometers

Abstract: In this paper we present a framework that allows for the automatic identification of sporting activities using commonly available smartphones. We extract discriminative informational features from smartphone accelerometers using the Discrete Wavelet Transform (DWT). Despite the poor quality of their accelerometers, smartphones were used as capture devices due to their prevalence in today's society. Successful classification on this basis potentially makes the technology accessible to both elite and non-elite athletes. Extracted features are used to train different categories of classifiers. No one classifier family has a reportable direct advantage in activity classification problems to date; thus we examine classifiers from each of the most widely used classifier families. We investigate three classification approaches; a commonly used SVM-based approach, an optimized classification model and a fusion of classifiers. We also investigate the effect of changing several of the DWT input parameters, including mother wavelets, window lengths and DWT decomposition levels. During the course of this work we created a challenging sports activity analysis dataset, comprised of soccer and field-hockey activities. The average maximum F-measure accuracy of 87% was achieved using a fusion of classifiers, which was 6% better than a single classifier model and 23% better than a standard SVM approach.

Impact of school inspections on improvement of schools-describing assumptions on causal mechanisms in six European countries

Abstract: School inspection is used by most European education systems as a major instrument for controlling and promoting the quality of schools. Surprisingly, there is little research knowledge about how school inspections drive the improvement of schools and which types of approaches are most effective and cause the least unintended consequences. The study presented in this paper uses interviews with inspection officials and a document analysis to reconstruct the “program theories” (i.e. the assumptions on causal mechanisms, linking school inspections to their intended outcomes of improved teaching and learning) of Inspectorates of Education in six European countries. The results section of the paper starts with a summary of the commonalities and differences of these six national inspection models with respect to standards and thresholds used, to types of feedback and reporting, and to the sanctions, rewards and interventions applied to motivate schools to improve. Next, the intermediate processes through which these inspection models are expected to promote good education (e.g. through actions of stakeholders) are explained. In the concluding section, these assumptions are critically discussed in the light of research knowledge.

Preparative Purification of Recombinant Proteins: Current Status and Future Trends

Abstract: Advances in fermentation technologies have resulted in the production of increased yields of proteins of economic, biopharmaceutical, and medicinal importance. Consequently, there is an absolute requirement for the development of rapid, cost-effective methodologies which facilitate the purification of such products in the absence of contaminants, such as superfluous proteins and endotoxins. Here, we provide a comprehensive overview of a selection of key purification methodologies currently being applied in both academic and industrial settings and discuss how innovative and effective protocols such as aqueous two-phase partitioning, membrane chromatography, and high-performance tangential flow filtration may be applied independently of or in conjunction with more traditional protocols for downstream processing applications.